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- PDB-3tvt: Structural basis for Discs Large interaction with Pins -

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Basic information

Entry
Database: PDB / ID: 3tvt
TitleStructural basis for Discs Large interaction with Pins
Components
  • Disks large 1 tumor suppressor protein
  • Partner of Inscuteable
KeywordsANTITUMOR PROTEIN/PROTEIN BINDING / Dlg / Src-homology-3 / Guanylate kinase / Phosphorylation-dependent / Cell membrane / ANTITUMOR PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


smooth septate junction / positive phototaxis / G alpha (i) signalling events / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly ...smooth septate junction / positive phototaxis / G alpha (i) signalling events / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / negative regulation of imaginal disc growth / Activation of Ca-permeable Kainate Receptor / morphogenesis of follicular epithelium / type Ib terminal bouton / subsynaptic reticulum / Synaptic adhesion-like molecules / establishment or maintenance of polarity of follicular epithelium / morphogenesis of larval imaginal disc epithelium / Unblocking of NMDA receptors, glutamate binding and activation / gravitaxis / tricellular tight junction / establishment of spindle orientation / anterior/posterior axis specification, follicular epithelium / negative regulation of peptidoglycan recognition protein signaling pathway / pole plasm protein localization / basal protein localization / asymmetric protein localization involved in cell fate determination / dorsal closure / follicle cell of egg chamber development / regulation of epidermal growth factor receptor signaling pathway / positive regulation of synaptic assembly at neuromuscular junction / asymmetric cell division / male courtship behavior / guanylate kinase activity / asymmetric neuroblast division / morphogenesis of a polarized epithelium / behavioral response to ethanol / receptor localization to synapse / apical cortex / leading edge membrane / apicolateral plasma membrane / synaptic assembly at neuromuscular junction / establishment or maintenance of epithelial cell apical/basal polarity / GDP-dissociation inhibitor activity / mating behavior / cell fate specification / receptor clustering / locomotor rhythm / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / neuroblast proliferation / postsynaptic density membrane / neuromuscular junction / terminal bouton / kinase binding / cell-cell adhesion / nervous system development / cell cortex / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / cytoskeleton / neuron projection / protein domain specific binding / synapse / perinuclear region of cytoplasm / signal transduction / membrane / plasma membrane
Similarity search - Function
GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Tetratricopeptide repeat / domain in receptor targeting proteins Lin-2 and Lin-7 ...GoLoco motif / L27-1 / GoLoco motif / L27_1 / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Tetratricopeptide repeat / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / Tetratricopeptide repeat / L27 domain profile. / L27 domain superfamily / Disks large 1-like / Tetratricopeptide repeat / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Disks large 1 tumor suppressor protein / Partner of Inscuteable / LD33695p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJohnston, C.A. / Doe, C.Q. / Prehoda, K.E.
CitationJournal: To be Published
Title: Structural basis for Discs Large interaction with Pins
Authors: Johnston, C.A. / Doe, C.Q. / Prehoda, K.E.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large 1 tumor suppressor protein
B: Partner of Inscuteable


Theoretical massNumber of molelcules
Total (without water)39,5862
Polymers39,5862
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.604, 94.546, 83.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Disks large 1 tumor suppressor protein


Mass: 33849.078 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dlg1, l(1)dlg1, CG1725 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31007
#2: Protein/peptide Partner of Inscuteable / Pins


Mass: 5737.344 Da / Num. of mol.: 1 / Fragment: linker domain (UNP residues 411-460) / Mutation: S436D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: raps, pins, CG5692 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NH88, UniProt: Q9VB22*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCS LARGE FRAGMENT COMPRISES SH3 DOMAIN (UNP RESIDUES 618-698) AND GUANYLATE KINASE-LIKE DOMAIN ...DISCS LARGE FRAGMENT COMPRISES SH3 DOMAIN (UNP RESIDUES 618-698) AND GUANYLATE KINASE-LIKE DOMAIN (UNP RESIDUES 762-970) WITH RESIDUES 699-761 DELETED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M NaCl, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 47972 / Num. obs: 45138 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 23.74 Å2 / Rsym value: 0.04 / Net I/σ(I): 55.4
Reflection shellResolution: 1.6→1.66 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.779 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24545 2400 5 %RANDOM
Rwork0.22016 ---
obs0.22141 45138 99.07 %-
all-47972 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 234 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222247
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9563032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0623.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8315408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211707
X-RAY DIFFRACTIONr_mcbond_it1.1241.51341
X-RAY DIFFRACTIONr_mcangle_it2.03522178
X-RAY DIFFRACTIONr_scbond_it3.143906
X-RAY DIFFRACTIONr_scangle_it5.084.5854
LS refinement shellResolution: 1.6→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 153 -
Rwork0.316 3102 -
obs--93.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.05072.60030.52655.07822.29831.45350.2109-0.2725-0.12990.0328-0.3118-0.10480.0026-0.21770.10080.1126-0.0886-0.01450.1223-0.04390.108628.630924.1232-1.6018
21.41110.08480.80910.42580.0581.45750.00690.04110.0864-0.0449-0.0074-0.08090.04170.2080.00050.0297-0.00310.02160.0415-0.01090.041517.55044.2467-18.1065
36.15412.9281-0.62699.297-2.83093.82820.22480.1699-0.7343-0.2256-0.389-0.63340.25530.85070.16420.07970.0393-0.03360.25410.00980.120817.9085-0.028-30.4665
432.9062-21.9124-21.402117.86715.940517.31260.2683-0.55121.71690.27520.0103-0.0439-1.45760.0074-0.27860.9913-0.0108-0.0410.29880.00330.606813.925817.4902-28.1459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A602 - 779
2X-RAY DIFFRACTION2A780 - 971
3X-RAY DIFFRACTION3B434 - 442
4X-RAY DIFFRACTION4B443 - 447

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